The cache, hidden in small containers in a van, was made up of wildlife from Australia, Indonesia and Papua New Guinea, said Eric Gallego, spokesman for the local office of the Department of Environment and Natural Resources.
They included yellow-crested cockatoos and long-beaked echidnas, two species listed as "critically endangered" by the International Union for the Conservation of Nature.
They also included four wallabies from Australia and about 90 exotic parrots from Indonesia, said Gallego.
Law enforcers acting on a tip stopped a van with the wildlife and two attendants in the southern city of Surigao on Mindanao island on Saturday, just as the vehicle was about to board a ship heading north.
The birds and animals are believed to have been shipped from Indonesia to Malaysia and then across the maritime border to the southern Philippines where they would be taken to Manila, said Gallego.
"There must have been an order from a rich person in Manila for the animals as collector's items. It must be someone who is into rare animals," he said.
Two men caught with the van will be charged with illegally transporting wildlife, a crime punishable up to six months in jail and a 50,000-peso (USD 1,120) fine depending on the rarity of the animals involved.
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